The historic rendezvous awash in symbolism as leaders of two of the biggest branches of Christianity holding a rare meeting in Communist Cuba.

Pope Francis and Russian Orthodox Church Patriarch Kiril held a historic meeting in Cuba on Friday, calling for unity and the protection of Christians persecuted in the Middle East.

The two leaders embraced and kissed each other as they held the first ever meeting between a Roman Catholic pope and a Russian Orthodox patriarch since the historic 11th century split between the eastern and the western branches of the church.

"I'm happy to greet you, dear brother," the Russian Church leader said, to which the Pope replied, "Finally!"

The meeting took place at a terminal of the Havana airport as the Pope was on his way to Mexico while the Patriarch had arrived for his visit of Cuba, Brazil and Paraguay.

The churches, which had split apart bitterly 1,000 years ago over differences of faith that came to be known as the 'great schism', have had no official contact in the last five centuries.

While the Roman Catholic Church that Francis has been heading since 2013 has more a billion worldwide followers, the Russian Orthodox Church, which is aligned to the Kremlin, has about 165 million faithful.

With the leaders of two of the biggest branches of Christianity holding a rare meeting in Cuba -- as the guests of a Communist government -- the historic rendezvous was awash in rich symbolism.

While Cuba is under the sphere of influence of Moscow, to which the Russian Orthodox Church is politically aligned, the vast majority of Cuban Christianity is Roman Catholic, coming under the spiritual leadership of the Pope in Rome.

Francis and Kiril issued a joint statement saying the meeting was a landmark in the re-establishment of "this unity wished for by God."

They also stressed the need to protect the faithful under assault around the world.

"In many countries of the Middle East and North Africa whole families, villages and cities of our brothers and sisters in Christ are being completely exterminated," indirectly referring to the Islamic State's rampage over the faith.

"Their churches are being barbarously ravaged and looted, their sacred objects profaned, their monuments destroyed."

Great schism of 1054

At the root of the 1,000-year frost in ties between the two churches is the great schism of 1054 when the Roman Pope Luiz IX and the Patriarch of Constantinople Cerularius excommunicated each other.

Many attempts at reunification in the following centuries failed. There were attempts to hold top-level talks in rcent history but these also did not materialise. The closest such plans came was the planned meeting between Pope John Paul II and Russian Orthodox Patriarch Alexy II in 1997. The meeting was, however, cancelled.